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Background. A local eutrophication process is noted for the first time in Listvennichnyi bay in Lake Baikal. High level of biogenic elements in the water of the bay led to nuisance growth of filamentous algae. Rapid identification of these algae's taxa was necessary to assess ecosystem damage in the polluted area of the lake. Materials and methods. We determined a boundary of bottom fouling by locating transects ranging from 0 to 10 meters in different areas of the bay. Algae samples were examined using microscopic techniques as well as SSU 18S rDNA sequencing. Phylogenetic trees were estimated using Bayesian inference (BI) based on SSU alignment. Results. Our results showed intensive filamentous algae fouling in depth from 3 to 10 meters along the coastline of the eastern part of the bay. Morphological and molecular analysis demonstrated prevalence in samples of Ulothrix zonata (Web. et Mohr) Kütz. Using SSU 18S rDNA sequencing data we also showed presence of three species of Spirogyra Link. genus. Conclusion. Detection of Spirogyra species which are normally not typical for such areas of the lake along with Ulothrix zonata extended more deeply than usually observed reveals severe phytocenosis disturbance of the polluted part of Lake Baikal.

During eukaryotic translation, peptides/proteins are created using L-amino acids. However, a D-amino acid-containing peptide (DAACP) can be produced through post-translational modification via an isomerase enzyme. General approaches to identify novel DAACPs and investigate their function, particularly in specific neural circuits, are lacking. This is primarily due to the difficulty in characterizing this modification and due to the limited information on neural circuits in most species. We describe a multipronged approach to overcome these limitations using the sea slug Aplysia californica. Based on bioinformatics and homology to known DAACPs in the land snail Achatina fulica, we targeted two predicted peptides in Aplysia, GFFD, similar to achatin-I (GdFAD versus GFAD, where dF stands for D-phenylalanine), and YAEFLa, identical to fulyal (YdAEFLa versus YAEFLa), using stereoselective analytical methods, i.e. MALDI MS fragmentation analysis and LC-MS/MS. Although YAEFLa in Aplysia was detected only in an all L-form, we found that both GFFD and GdFFD were present in the Aplysia CNS. In situ hybridization and immunolabeling of GFFD/GdFFD-positive neurons and fibers suggested that GFFD/GdFFD might act as an extrinsic modulator of the feeding circuit. Consistent with this hypothesis, we found that GdFFD induced robust activity in the feeding circuit and elicited egestive motor patterns. In contrast, the peptide consisting of all L-amino acids, GFFD, was not bioactive. Our data indicate that the modification of an L-amino acid-containing neuropeptide to a DAACP is essential for peptide bioactivity in a motor circuit, and thus it provides a functional significance to this modification.

The propagation of ultrashort optical pulses in planar chalcogenide glass waveguides with uniform or periodic claddings is considered. In comparison with silica waveguides a structure based on chalcogenide glass provides higher nonlinearity. This material has a high normal dispersion in the wavelength range of 1.5–3.5 μm. Periodic waveguide structures can be used to compensate for this dispersion. High-intensity laser pulses propagating in these structures undergo spectral broadening. The influence of the phase self-modulation of a pulse on its spectrum and width is analyzed using numerical simulations.

Waveguide losses in all-solid photonic bandgap fibre are studied numerically using both vectorial mode solver and vectorial beam propagation methods. Confinement loss, including material losses, is comprehensively evaluated for defect modes of hexagonal lattice photonic bandgap fibre. The excitation of the index-guiding modes at the bandgap edges leads to a narrowing of the transmission bands. Submicron deformations of the transverse structure of the fibre lead to a significant reduction in the width of the transmission bands, yet the minimum value of the losses within these bandgaps remains practically unchanged. Longitudinal variation of the fibre profile increases the effective losses by up to tens of dB/m.

Tag7 (PGRP-S or PGLYRP1), while possessing an antimicrobial activity, also exhibits an antitumor effect when in complex with the major heat shock protein Hsp70. The cytotoxic Tag7-Hsp70 complex is secreted by lymphocytes after interaction with the HLA-negative tumors. Previously, we have shown that IL-2 induces formation of the CD4

An important problem in cellular immunology is to identify new populations of cytotoxic lymphocytes capable of killing tumor cells that have lost classical components of MHC-machinery and to understand mechanisms of the death of these cells. We have previously found that CD4

The packaging of DNA into chromatin plays an important role in the fidelity of DNA-related processes. The position of nucleosomes, covalent histone modifications, and the integrity of individual histone proteins all contribute to the accessibility and function of DNA. Histones and their modifications influence the expression of genes both positively and negatively and act at the initiation, elongation, and termination stages of transcription. One such modification, methylation of lysine 36 on histone H3 (H3K36), catalyzed by the Set2 histone methyltransferase (KMT3), is associated with the elongation phase of transcription and is found within the coding regions of actively transcribed genes (19, 24, 25, 39, 41, 42, 46). Set2 catalyzes all three states of methylation at H3K36, monomethyl (me1), dimethyl (me2), and trimethyl (me3), and negatively influences gene expression (20), including the repression of cryptic promoters within the coding region of genes such as STE11 (5, 11, 23). Repression is proposed to result from recruitment of the Rpd3S histone deacetylase complex to specific modifications on the chromatin, including an interaction between methylated H3K36 and the chromodomain of Eaf3, leading to deacetylation and stabilization of newly transcribed chromatin, particularly on poorly expressed genes (5, 11, 15, 22, 23). The presence of H3K36me2 correlates with whether a gene is expressed or not (39), while H3K36me3 tends to correlate with highly expressed genes (38), supporting distinct functions for the two modifications. Analysis of the C-terminal SRI domain of Set2 indicates that it interacts with the phosphorylated carboxy-terminal domain (CTD) of Rbp1(26, 45), the largest subunit of RNA polymerase II (RNAPII), and is required for normal levels of H3K36me (16). This interaction supports cotranscriptional deposition of methyl groups on H3K36 during transcription elongation. Further support for H3K36 methylation being a cotranscriptional modification comes from observations that Ctk1, a subunit of a cyclin-dependent kinase complex (CTD-K) that acts on the CTD of Rbp1 within RNAPII (6, 21, 36, 46), and Spt6, a transcription elongation factor (4, 9, 10, 14), are required for H3K36 methylation (8, 15, 19, 47) and for repression of the cryptic promoters at STE11 (5). Spt6 is an essential protein that binds to histone H3 and is capable of nucleosome assembly in vitro (4). Spt6 is known to control the initiation (1), elongation (10, 13, 14, 18, 27), and termination (12) phases of transcription, including cotranscriptional pre-mRNA processing and export (48). The protein has several domains, including an EF hand, a resolvase domain, a helix-hairpin-helix DNA binding domain, and an SH2 domain. The SH2 domain of mammalian Spt6 binds to the CTD on RNAPII when phosphorylated at Ser2 (48). In Saccharomyces cerevisiae, the requirement for Spt6 in maintaining H3K36 methylation is allele specific (8). Strains expressing the spt6-140 allele show normal levels of H3K36 methylation, while those expressing the spt6-1004 allele show defects in H3K36 dimethylation and trimethylation. At present it is not known if the different methylation states at H3K36 are associated with different functions, although there are functions associated with Set2 that are likely to be independent of the Rpd3S complex and cotranscriptional histone deacetylation (3, 43, 44). Moreover, it is not known if Set2 KMTase activity is regulated in any way. Here we show that the region of Set2 (1-261) containing the SET domain is sufficient for H3K36me2, histone deacetylation, and repression of cryptic promoters at STE11 but not for H3K36me3. Moreover, Set2-catalyzed H3K36me2 is largely independent of Ctk1-dependent CTD phosphorylation and the SRI domain of Set2, consistent with the observations that H3K36me2 correlates with whether a gene is “on” or “off,” but not the level of activity of a gene (39). By contrast, H3K36me3 requires the integrity of H3P38, Spt6, the CTD of RNAPII, Ctk1, and the SRI domain of Set2. These data indicate that the different methylation states created by the Set2 KMTase are likely to be regulated and are functionally distinct.

An interferometric pump-probe method with the femtosecond resolution in time is used to study the third-order non-linear optical response and photosensitivity of a variety of chalcogenide glasses of the system As-S-Se.

An important problem of investigation of the air and water contamination by the mid-IR spectroscopy is discussed. A model of evanescent wave sensor made of a multimode waveguide transparent in the mid-IR spectral range is developed. Transmittance and sensitivity of a sensing element consisting of an input chalcogenide waveguide and a sensing waveguide depend on distribution of the guided modes amplitudes in the sensing waveguide. We have demonstrated that excitation of higher-order modes is important for optimal performance of such a sensor.

Background Cichlid fishes have evolved remarkably diverse reproductive, social, and feeding behaviors. Cell-to-cell signaling molecules, notably neuropeptides and peptide hormones, are known to regulate these behaviors across vertebrates. This class of signaling molecules derives from prohormone genes that have undergone multiple duplications and losses in fishes. Whether and how subfunctionalization, neofunctionalization, or losses of neuropeptides and peptide hormones have contributed to fish behavioral diversity is largely unknown. Information on fish prohormones has been limited and is complicated by the whole genome duplication of the teleost ancestor. We combined bioinformatics, mass spectrometry-enabled peptidomics, and molecular techniques to identify the suite of neuropeptide prohormones and pituitary peptide products in Astatotilapia burtoni, a well-studied member of the diverse African cichlid clade. Results Utilizing the A. burtoni genome, we identified 148 prohormone genes, with 21 identified as a single copy and 39 with at least 2 duplicated copies. Retention of prohormone duplicates was therefore 41 %, which is markedly above previous reports for the genome-wide average in teleosts. Beyond the expected whole genome duplication, differences between cichlids and mammals can be attributed to gene loss in tetrapods and additional duplication after divergence. Mass spectrometric analysis of the pituitary identified 620 unique peptide sequences that were matched to 120 unique proteins. Finally, we used in situ hybridization to localize the expression of galanin, a prohormone with exceptional sequence divergence in cichlids, as well as the expression of a proopiomelanocortin, prohormone that has undergone an additional duplication in some bony fish lineages. Conclusion We characterized the A. burtoni prohormone complement. Two thirds of prohormone families contain duplications either from the teleost whole genome duplication or a more recent duplication. Our bioinformatic and mass spectrometric findings provide information on a major vertebrate clade that will further our understanding of the functional ramifications of these prohormone losses, duplications, and sequence changes across vertebrate evolution. In the context of the cichlid radiation, these findings will also facilitate the exploration of neuropeptide and peptide hormone function in behavioral diversity both within A. burtoni and across cichlid and other fish species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2914-9) contains supplementary material, which is available to authorized users.

d-Aspartate (d-Asp) is found in specific neurons, transported to neuronal terminals and released in a stimulation-dependent manner. Because d-Asp formation is not well understood, determining its function has proved challenging. Significant levels of d-Asp are present in the cerebral ganglion of the F- and C-clusters of the invertebrate Aplysia californica, and d-Asp appears to be involved in cell-cell communication in this system. Here, we describe a novel protein, DAR1, from A. californica that can convert aspartate and serine to their other chiral form in a pyridoxal 5′-phosphate (PLP)-dependent manner. DAR1 has a predicted length of 325 amino acids and is 55% identical to the bivalve aspartate racemase, EC 5.1.1.13, and 41% identical to the mammalian serine racemase, EC 5.1.1.18. However, it is only 14% identical to the recently reported mammalian aspartate racemase, DR, which is closely related to glutamate-oxaloacetate transaminase, EC 2.6.1.1. Using whole-mount immunohistochemistry staining of the A. californica central nervous system, we localized DAR1-like immunoreactivity to the medial region of the cerebral ganglion where the F- and C-clusters are situated. The biochemical and functional similarities between DAR1 and other animal serine and aspartate racemases make it valuable for examining PLP-dependent racemases, promising to increase our knowledge of enzyme regulation and ultimately, d-serine and d-Asp signaling pathways.

Chalcogenide glasses are ideal materials for developing fiber lasers and amplifiers, remote sensors, high-speed switches, and other devices that operate in the IR range of 1–10 μm. The nonlinear refractive index of chalcogenide glasses may exceed that of quartz glass by a factor of 100–1200 or even more. The data on the dispersion properties of some chalcogenide glass compositions in the IR range are presented. The possibility of forming waveguide structures with specified dispersion properties (in particular with a fixed wavelength at which the group velocity dispersion is zero) from these glasses is numerically investigated. It is shown by the example of completely glassy periodic waveguide structures with planar geometry that the use of photonic band gap modes makes it possible the change the position of zero dispersion in a wide wavelength range. In the calculations the contrast of waveguide structures was varied using parameters of glasses of different composition.

Here we investigated the ability of the human X-family DNA polymerases beta and lambda to bypass thymine glycol (Tg) in gapped DNA substrates with the damage located in a defined position of the template strand. Maximum velocities and the Michaelis constant values were determined to study DNA synthesis in the presence of either Mg(2+) or Mn(2+). Additionally, the influence of hRPA (human replication protein A) and hPCNA (human proliferating cell nuclear antigen) on TLS (translesion synthesis) activity of DNA polymerases beta and lambda was examined. The results show that (i) DNA polymerase lambda is able to catalyze DNA synthesis across Tg, (ii) the ability of DNA polymerase lambda to elongate from a base paired to a Tg lesion is influenced by the size of the DNA gap, (iii) hPCNA increases the fidelity of Tg bypass and does not influence normal DNA synthesis catalyzed by DNA polymerase lambda, (iv) DNA polymerase beta catalyzes the incorporation of all four dNTPs opposite Tg, and (v) hPCNA as well as hRPA has no specific effect on TLS in comparison with the normal DNA synthesis catalyzed by DNA polymerase beta. These results considerably extend our knowledge concerning the ability of specialized DNA polymerases to cope with a very common DNA lesion such as Tg.

Genomes of four tick-borne encephalitis virus strains, isolated from the blood of the individuals after tick bites and causing no clinical symptoms of infection, were characterized. Analysis of translated polypeptides revealed 21 amino acid positions typical of this group of strains and distinguishing them from the other tick-borne encephalitis virus strains of Far Eastern subtype examined earlier. Only three mutations led to substantial amino acid changes, which probably could affect the infection process severity. It is suggested that two associated mutations, deletion of amino acid 111 in the capsid protein C and substitution (Ser1534 → Phe) in the NS3 protein influence strictly coordinated polyprotein processing, disturbing correct arrangement of viral particles. This process can result in the development of defect viral particles, containing no RNA. Mutation (Ser917 → Gly) in nonstructural protein NS1 results in the substitution of hydrophilic amino acid, specific to highly virulent strains, by the hydrophobic one. This could influence the effectiveness of viral replication complex, thereby affecting the infectivity of tick-borne encephalitis virus strains.

High-rise apartment houses have technical and economic advantages in areas with dense population. Their placement in the central part of the city allows increasing the number of living space in the limited territory, to bring population to the place of employment and reduce pendular migration. But increase in population density leads to psychological problems: level of a stress, fatigue increases, the number of phobias grows, infectious diseases extend quicker. These problems can be solved at resettlement of inhabitants to the suburb. However such decision leads to aggravation of a transport problem and the pulsing increase in population density in the downtown and on its suburb. To solve a transport problem, it is necessary not to increase the square of the cities. Therefore in the suburbs is also used high-rise construction. But high-rise residential districts on the suburb of the city get own social problems which are capable to destroy all advantages of high-rise construction.

DNA demethylation in mammalia occurs after fertilization and during embryogenesis and accompanies cell aging and cancer transformation. With the help of the primer extension reaction, MALDI MS and DNA cleavage by thymine DNA glycosylase deamination of 5-methylcytosine residues has been shown to take place when the model methylated DNA duplexes are treated with nuclear extracts from the cell lines СНO, HeLa, and Skov3. The hypothesis that deamination of 5-methylcytosine is the first stage of demethylation in mammalia has been postulated.

Nitric oxide (NO), an intercellular signaling molecule, helps coordinate neuronal network activity. Here we examine NO generation in the Aplysia central nervous system using 4,5-diaminofluorescein diacetate (DAF-2 DA), a fluorescent reagent that forms 4,5-diaminofluorescein triazole (DAF-2T) upon reaction with NO. Recognizing that other fluorescence products are formed within the biochemically complex intracellular environment, we validate the observed fluorescence as being from DAF-2T; using both capillary electrophoresis and mass spectrometry we confirm that DAF-2T is formed from tissues and cells exposed to DAF-2 DA. We observe three distinct subcellular distributions of fluorescence in neurons exposed to DAF-2 DA. The first shows uniform fluorescence inside the cell, with these cells being among previously confirmed NOS-positive regions in the Aplysia cerebral ganglion. The second, seen inside buccal neurons, exhibits point sources of fluorescence, 1.5 ± 0.7 µm in diameter. Interestingly, the number of fluorescence puncta increases when the tissue is preincubated with the NOS substrate L-arginine, and they disappear when cells are preexposed to the NOS inhibitor L-NAME, demonstrating that the fluorescence is connected to NOS-dependent NO production. The third distribution type, seen in the R2 neuron, also exhibits fluorescent puncta, but only on the cell surface. Fluorescence is also observed in the terminals of cultured bag cell neurons loaded with DAF-2 DA. Surprisingly, fluorescence at the R2 surface and bag cell neuron terminals is not modulated by L-arginine or L-NAME, suggesting it has a source distinct from the buccal and cerebral ganglion DAF 2T-positive tissues.

Neuropeptides are a diverse set of complex cell-cell signaling molecules that modulate behavior, learning, and memory. Their spatially heterogeneous distributions, large number of post-translational modifications, and wide range of physiologically active concentrations make their characterization challenging. Matrix-assisted laser desorption/ionization (MALDI) mass spectrometric imaging is well-suited to characterizing and mapping neuropeptides in the central nervous system. Because matrix application can cause peptide migration within tissue samples, application parameters for MALDI typically represent a compromise between attaining the highest signal quality and preserving native spatial distributions. The stretched sample approach minimizes this trade-off by fragmenting the tissue section into thousands of spatially isolated islands, each approximately 40 mum in size. This inhibits analyte migration between the pieces and, at the same time, reduces analyte-salt adduct formation. Here, we present methodological improvements that enable the imaging of stretched tissues and reveal neuropeptide distributions in nervous tissue from Aplysia californica. The distributions of known neuropeptides are shown to correspond with previous immunohistochemical results, demonstrating that the stretched imaging method is well-suited for working with easily redistributed molecules and heterogeneous tissues and reduces adducts from physiological salts.

The properties of highly nonlinear glasses for photonic devices and the advantages of processing these materials using femtosecond laser pulses are discussed in a brief review. A novel approach is proposed for the optimization of the modification process that takes into account the dispersion of the nonlinear coefficients of refraction and absorption. Numerical modeling of the pulse energy deposition into a sample of chalcogenide glass shows that the shapes and dimensions of the modified regions depend on the nonlinear coefficients.

Thymidine glycol residues in DNA are biologically active oxidative molecular damage sites caused by ionizing radiation and other factors. One or two thymidine glycol residues were incorporated in 19- to 31-mer DNA fragments during automatic oligonucleotide synthesis. These oligonucleotide models were used to estimate the effect of oxidized thymidines on the thermodynamic, substrate and interfacial acoustic properties of DNA. UV-monitoring melting data revealed that modified residues in place of thymidines destabilize the DNA double helix by 8-22 degrees C, depending on the number of lesions, the length of oligonucleotide duplexes and their GC-content. The diminished hybridizing capacity of modified oligonucleotides is presumably due to the loss of aromaticity and elevated hydrophilicity of thymine glycol in comparison to the thymine base. According to circular dichroism (CD) data, the modified DNA duplexes retain B-form geometry, and the thymidine glycol residue introduces only local perturbations limited to the lesion site. The rate of DNA hydrolysis by restriction endonucleases R.MvaI, R.Bst2UI, R.MspR9I and R.Bme1390I is significantly decreased as the thymidine glycol is located in the central position of the double-stranded recognition sequences 5'-CC / WGG-3' (W = A, T) or 5'-CC / NGG-3' (N = A, T, G, C) adjacent to the cleavage site. On the other hand, the catalytic properties of enzymes R.Psp6I and R.BstSCI recognizing the similar sequence are not changed dramatically, since their cleavage site is separated from the point of modification by several base-pairs. Data obtained by gel-electrophoretic analysis of radioactive DNA substrates were confirmed by direct spectrophotometric assay developed by the authors. The effect of thymidine glycol was also observed on DNA hybridization at the surface of a thickness-shear mode acoustic wave device. A 1.9-fold decrease in the rate of duplex formation was noted for oligonucleotides carrying one or two thymidine glycol residues in relation to the unmodified analog.

The local heating of glass by a focused femtosecond laser pulse and cooling of an irradiated region are numerically modeled. The structural modifications that change the optical properties of glass are assumed to occur within a bulk region whose temperature after irradiation exceeds the glass transition temperature. The shape of the modified region obtained from the calculations coincides with that known from experimental data available. The size of this region is determined by the spatiotemporal dynamics of the laser beam under multiphoton absorption conditions. The heating of glass is maximal in front of a thin lens used for the beam focusing.

The isolation and extraction of natively occurring signaling peptides (SPs) from tissue is a critical first step in characterizing these peptides. Recent studies have outlined several approaches designed to preserve and extract SPs from tissue. Here, we demonstrate a surprisingly simple method to extract SPs from tissue samples, ranging from cell clusters to brain punches to intact brain regions, using a matrix often employed in matrix-assisted laser desorption/ionization mass spectrometry-2,5-dihydroxybenzoic acid (DHB). DHB allows for the effective extraction of endogenous peptides from tissue as well as long-term preservation of tissue samples and extracts. Using the mouse pituitary gland as a model, the extraction protocol effectively recovers 24 known and many additional putative peptides from individual samples. Peptide extracts stored in the DHB extraction media are stable for years without freezing. The approach is also effective for other neuronal tissues; the complement of neuropeptides in bag cell neuron clusters from the Aplysia central nervous system, the rat cerebellum, and rat dorsal striatum also have been examined. Advantages of this new extraction procedure are its technical simplicity, reproducibility, ease of remote preparation of samples, and long-term sample preservation without freezing.

The propagation of a non-stationary light beam through a linear/non-linear discontinuity in a planar waveguide is considered by using an approximate approach based on the Generalised Non-Linear Schrodinger Equation (GNLSE) and the rigorous Transmission Line Modelling (TLM) Method. The objective is to compare the different theoretical approaches that can be used for the design of guiding structures with pulse shaping and signal processing functionality. Reflection and transmission of the light beam propagating through the junction of linear and non-linear waveguides are studied with respect to a dimensionless parameter that defines the increase of the refractive index induced by high-intensity radiation. In conclusion, the routes to efficient modelling are discussed.

Interfacing nanoscale elements into a microfluidic device enables a new range of fluidic manipulations. Nanocapillary array membranes (NCAMs), consisting of thin (5 micromd20 microm) membranes containing arrays of nanometer diameter (10 nma500 nm) pores, are a convenient method of interfacing vertically separated microchannels in microfluidic devices that allow the external control of analyte transport between microfluidic channels. To add functionality to these nanopores beyond simple fluid transport, here we incorporate an antibody-based molecular recognition element onto the pore surface that allows selective capture, purification, and release of specific analytes from a mixture. The pores are fabricated by electroless plating of gold into the nanopores of an NCAM (Au-NCAM). An antibody is then immobilized on the Au-NCAM via gold-thiol chemistry as a thiolated fragment of antigen-binding (Fab') prepared by direct digestion of the antibody followed by reduction of the disulfide linkage on the hinge region. The successful immobilization and biological activity of the resultant Fab' through this protocol is verified on planar gold by fluorescence microscopy, scanning electron microscopy, and atomic force microscopy. Selective capture and release of human insulin is verified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. The relative mass spectral peak intensities for insulin versus nonantigenic peptides increase more than 20-fold after passing through the Fab'-Au-NCAM relative to the control Au-NCAM. The affinity-tagged Au-NCAM can be incorporated into microfluidic devices to allow the concentration, capture, and characterization of analytes in complex mixtures with high specificity.

Integration of human immunodeficiency virus type 1 DNA into the infected cell genome is one of the key steps of the viral replication cycle. Therefore, viral integrase is of interest as a target for new antiviral drugs. Conjugates of 11-mer single-stranded oligonucleotides with hydrophobic molecules were shown to be efficient integrase inhibitors, inducing dissociation of the integrase-viral DNA complex. The dependence of the conjugate inhibitory activity on the oligonucleotide length and structure as well as on the structure of hydrophobic molecules was studied. Conjugates with eosin and oleic acid proved to be the most active. Conjugates of these molecules with 2′-O-methyl-oligonucleotide inhibited integrase at concentrations 50–100 nM but did not influence some other DNA-binding enzymes.

In molecular biology, the production of proteins can be effectively inhibited by introducing specific oligonucleotides into a living cell (gene silencing or antisense strategy; important for gene therapy). Calcium phosphate nanoparticles can serve as carriers for biomolecules in such therapeutic applications due to their high biocompatibility and biodegradability. Stable colloids were prepared by coating the inorganic nanoparticles with single- and double-stranded oligonucleotides. The dispersions were analysed by dynamic light scattering, zeta potential measurements, transmission electron microscopy, and scanning electron microscopy. Particles with a diameter of about 100 nm were obtained under optimized conditions. The efficiency of such nanoparticles to specifically inhibit protein synthesis was tested on HeLa-EGFP cells whose green fluorescence was turned off by the coated nanoparticles (gene silencing with siRNA). If siRNA was incorporated into the calcium phosphate particle and thereby protected from intracellular degradation, the transfection efficiency was significantly increased. The dispersions were stable and could be stored at 4 °C without loss of activity for several weeks, making them available as biochemical reagents.

Splice-variant products of the R15 neuropeptide gene are differentially expressed within the CNS of Aplysia. The goal of this study was to test whether the neurons in the abdominal ganglion that express the peptides encoded by this gene are part of a common circuit. Expression of R15 peptides had been demonstrated previously in neuron R15. Using a combination of immunocytochemical and analytical methods, this study demonstrated that R15 peptides are also expressed in heart exciter neuron RBHE, the two L9Ggill motoneurons, and L40—a newly identified interneuron. Mass spectrometric profiling of individual neurons that exhibit R15 peptide-like immunoreactivity confirmed the mutually exclusive expression of two splice-variant forms of R15 peptides in different neurons. The L9Gcells were found to co-express pedal peptide in addition to the R15 peptides. The R15 peptide-expressing neurons examined here were shown to be part of an autonomic control circuit that is active during fictive locomotion. Activity in this circuit contributes to implementing a central command that may help to coordinate autonomic activity with escape locomotion. Chronic extracellular nerve recording was used to determine the activity patterns of a subset of neurons of this circuit in vivo. These results demonstrate the potential utility of using shared patterns of neuropeptide expression as a guide for neural circuit identification.

Bioactive peptides (i.e., neuropeptides or peptide hormones) represent the largest class of cell-cell signaling molecules in metazoans and are potent regulators of neural and physiological function. In vertebrates, peptide hormones play an integral role in endocrine signaling between the brain and the gonads that controls reproductive development, yet few of these molecules have been shown to influence reproductive development in invertebrates. Here, we define a role for peptide hormones in controlling reproductive physiology of the model flatworm, the planarian Schmidtea mediterranea. Based on our observation that defective neuropeptide processing results in defects in reproductive system development, we employed peptidomic and functional genomic approaches to characterize the planarian peptide hormone complement, identifying 51 prohormone genes and validating 142 peptides biochemically. Comprehensive in situ hybridization analyses of prohormone gene expression revealed the unanticipated complexity of the flatworm nervous system and identified a prohormone specifically expressed in the nervous system of sexually reproducing planarians. We show that this member of the neuropeptide Y superfamily is required for the maintenance of mature reproductive organs and differentiated germ cells in the testes. Additionally, comparative analyses of our biochemically validated prohormones with the genomes of the parasitic flatworms Schistosoma mansoni and Schistosoma japonicum identified new schistosome prohormones and validated half of all predicted peptide-encoding genes in these parasites. These studies describe the peptide hormone complement of a flatworm on a genome-wide scale and reveal a previously uncharacterized role for peptide hormones in flatworm reproduction. Furthermore, they suggest new opportunities for using planarians as free-living models for understanding the reproductive biology of flatworm parasites.

The discovery of neuropeptides as signaling molecules with paracrine or hormonal regulatory functions has led to trailblazing advances in physiology and fostered the characterization of numerous neuropeptide-binding G protein-coupled receptors (GPCRs) as potential drug targets. The impact on human health has been tremendous: approximately 30% of commercial drugs act via the GPCR pathway. However, about 25% of the GPCRs encoded by the mammalian genome still lack their pharmacological identity. Searching for the orphan GPCR endogenous ligands that are likely to be neuropeptides has proved to be a formidable task. Here we describe the mass spectrometry (MS)-based technologies and experimental strategies that have been successful in achieving high-throughput characterization of endogenous peptides in nervous and endocrine systems.

The dorsal root ganglion (DRG) and its anatomically and functionally associated spinal nerve and ventral and dorsal roots are important components of the peripheral sensory-motor system in mammals. The cells within these structures use a number of peptides as intercellular signaling molecules. We performed a variety of mass spectrometry (MS)-based characterizations of peptides contained within and secreted from these structures, and from isolated and cultured DRG cells. Liquid chromatography-Fourier transform MS was utilized in DRG and nerve peptidome analysis. In total, 2724 peptides from 296 proteins were identified in tissue extracts. Neuropeptides are among those detected, including calcitonin gene-related peptide I, little SAAS, and known hemoglobin-derived peptides. Solid phase extraction combined with direct matrix-assisted laser desorption/ionization time-of-flight MS was employed to investigate the secretome of these structures. A number of peptides were detected in the releasate from semi-intact preparations of DRGs and associated nerves, including neurofilament- and myelin basic protein-related peptides. A smaller set of analytes was observed in releasates from cultured DRG neurons. The peptide signals observed in the releasates have been mass-matched to those characterized and identified in homogenates of entire DRGs and associated nerves. This data aids our understanding of the chemical composition of the mammalian peripheral sensory-motor system, which is involved in key physiological functions such as nociception, thermoreception, itch sensation, and proprioception.

Cell-to-cell variability and functional heterogeneity are integral features of multicellular organisms. Chemical classification of cells into cell type is important for understanding cellular specialization as well as organismal function and organization. Assays to elucidate these chemical variations are best performed with single cell samples because tissue homogenates average the biochemical composition of many different cells and oftentimes include extracellular components. Several single cell microanalysis techniques have been developed but tend to be low throughput or require preselection of molecular probes that limit the information obtained. Mass spectrometry (MS) is an untargeted, multiplexed, and sensitive analytical method that is well-suited for studying chemically complex individual cells that have low analyte content. In this work, populations of cells from the rat pituitary, the rat pancreatic islets of Langerhans, and from the Aplysia californica nervous system, are classified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI) MS by their peptide content. Cells were dispersed onto a microscope slide to generate a sample where hundreds to thousands of cells were separately located. Optical imaging was used to determine the cell coordinates on the slide, and these locations were used to automate the MS measurements to targeted cells. Principal component analysis was used to classify cellular subpopulations. The method was modified to focus on the signals described by the lower principal components to explore rare cells having a unique peptide content. This approach efficiently uncovers and classifies cellular subtypes as well as discovers rare cells from large cellular populations.

In modern Russia Centers of Social Assistance to Family and Children (CSAFC) are increasingly important in the field of psycho-pedagogical assistance and support to tutorial families bringing children-orphans up. The article analyzes long-term work experience (1998–2014 years) of these centers professionals on the implementation of socio-pedagogical support of child`s upbringing in a tutorial family technology. The authors have designed, substantiated and experimentally tested in real life a model of process of socio-pedagogical support of child`s upbringing in a tutorial family in some CSAFC. The article states that the model is implemented in stages (diagnostic stage, prognostic stage, adaptation and developmental stage, and result-final stage) and under some conditions (situational and environmental conditions, administrative and organizational, professional and personal conditions). The article analyzes the results of experimental work of socio-pedagogical support of child`s upbringing process in a tutorial family by CSAFC specialists. The results of a formative pedagogical experiment were: a) family climate improvement, positive emotional background strengthening in the relationship between caregivers and children, family trust improving; b) positive dynamics of type of family upbringing of a tutorial child (the authors have identified adaptive empirical type, constructive and pragmatic style, harmonious type); c) raising aspirations of tutors to cooperate with CSAFC specialists, to participate in collective creative activity together with a child on the basis of CSAFC; d) socio-pedagogical culture improving of tutors (the authors define the initial level, discrete level, sintonic level). DOI: 10.5901/mjss.2015.v6n3s3p165

Neurochemical differences in the hypothalamic-pituitary axis between individuals and between ages may contribute to differential susceptibility to cocaine abuse. This study measured peptide levels in the pituitary gland (Pit) and lateral hypothalamus (LH) in adolescent (age 30 days) and adult (age 65 days) mice from four standard inbred strains, FVB/NJ, DBA/2J, C57BL/6J, and BALB/cByJ, which have previously been characterized for acute locomotor responses to cocaine. Individual peptide profiles were analyzed using mass spectrometric profiling and principal component analysis. Sequences of assigned peptides were verified by tandem mass spectrometry. Principal component analysis classified all strains according to their distinct peptide profiles in Pit samples from adolescent mice, but not adults. Select pro-opiomelanocortin-derived peptides were significantly higher in adolescent BALB/cByJ and DBA/2J mice than in FVB/NJ or C57BL/6J mice. A subset of peptides in the LH, but not in the Pit, was altered by cocaine in adolescents. A 15 mg/kg dose of cocaine induced greater peptide alterations than a 30 mg/kg dose, particularly in FVB/NJ animals, with larger differences in adolescents than adults. Neuropeptides in the LH affected by acute cocaine administration included pro-opiomelanocortin-, myelin basic protein-, and glutamate transporter-derived peptides. The observed peptide differences could contribute to differential behavioral sensitivity to cocaine among strains and ages. Peptides were measured using mass spectrometry (MALDI-TOF) in individual lateral hypothalamus and pituitary samples from four strains and two ages of inbred mice in response to acute cocaine administration. Principal component analyses (PCA) classified the strains according to their peptide profiles from adolescent mice, and a subset of peptides in the lateral hypothalamus was altered by cocaine in adolescents.

Highly non-linear chalcogenide glasses are considered as a prospective material for frequency comb generation in optical microresonators. Using of a 2D microresonator for tailoring the normal material dispersion of chalcogenide glass is analyzed by evaluation of the group velocity dispersion coefficient in near- and mid- infrared. This is done for both approximate and accurate modal resonances of the whispering gallery modes of a 2D circular chalcogenide resonators. The results show that the using of a chalcogenide resonator extends the spectral range of normal dispersion regime to longer wavelengths.

Currently systematic passage social workers training courses and professional training is regarded as one of the necessary conditions for improving their professional competence, professional culture and personal development, as well as enhance their competitiveness in today’s job market. In modern Russia the question about the quality of the implementation of training courses and professional training of these specialists had never been more relevant. The article states that the current approaches to the problem provide an objective assessment of the quality of postgraduate professional education professionals social profile is largely based: a) on the basic provisions of the theory of educational measurement, b) on the basic provisions of the didactic and didactic testology taxonomy, c) to theory of independence procedures of expert assessments; d) on the methods of mathematical statistics; e) The pedagogical paradigm of quality management functioning educational systems, f) on the ideas of standardization of educational processes. The article reveals the essence of qualimetric techniques that the authors for eight years (2006-2014 years) has been successfully used for the objective evaluation of the quality of professional training courses of social work professionals. Particular attention is paid to the application qualimetric methods in the evaluation of the test results of student course preparation. The authors argue that the application of mathematical methods in the system of postgraduate education to assess the level of professional training of trainees help improve the quality of adult learning.

In this study, we present a complete mitochondrial genome of a deep-water amphipoda Brachyuropus grewingkii (Dybowsky, 1874) from Lake Baikal. A circular mitochondrial DNA has 17,118 bp in length and contains 13 protein-coding genes, two ribosomal RNA genes, 22 transfer RNA genes, a putative control region, and five intergenic spacers. An extended control region and altered positions of some tRNA genes distinguish mitochondrial genome of B. grewingkii from the mitochondrial genomes described for other Baikalian amphipoda species.

137 This article addresses methodology of modern landscape studies from the perspective of natural and man-made components of a territory. Railway infrastructure is not only an important systembuilding element of economic and settlement patterns; it also affects cultural landscapes. The study of cartographic materials and historiography made it possible to identify the main stages of the development of the Kaliningrad railway network in terms of its territorial scope and to describe causes of the observed changes. Historically, changes in the political, economic, and military environment were key factors behind the development of the Kaliningrad railway network. Nature was less important. The existing Kaliningrad railway network is to a great degree the legacy of the earlier, pre-war times. Today, its primary function is to provide international cargo and passenger transportation. Two types of railway infrastructure are identified in the Kaliningrad region — modern (functioning) and relic (abandoned) ones. In the Kaliningrad region, the process of land reclamation of the railway system starts when the maintenance of railroads is discontinued, which is followed by the formation of primitive soils and emerging biocenoses enhanced by fill soils and artificial relief.

Cryptic unstable transcripts (CUTs) are widely distributed in the genome of S. cerevisiae. These RNAs generally derive from nonannotated regions of the genome and are degraded rapidly and efficiently by the nuclear exosome via a pathway that involves degradative polyadenylation by a new poly(A) polymerase borne by the TRAMP complex. What is the share of significant information that is encrypted in CUTs and what distinguishes a CUT from other Pol II transcripts are unclear to date. Here we report the dissection of the molecular mechanism that leads to degradation of a model CUT, NEL025c. We show that the Nrd1p-Nab3p-dependent pathway, involved in transcription termination of sno/snRNAs, is required, albeit not sufficient, for efficient degradation of NEL025c RNAs and at least a subset of other CUTs. Our results suggest an important role for the Nrd1p-Nab3p pathway in the control of gene expression throughout the genome.

International audience; The human immunodeficiency virus type 1 (HIV-1) integrase is an essential enzyme in the life cycle of the virus and is therefore an attractive target for the development of new antiviral drugs. Among them, inhibitors which are capable of targeting the preassembled integrase/DNA complex are of particular interest, because they could suppress integrase activity in the context of the HIV-1 preintegration complex. Here, we study the mechanism of action of 11-mer oligonucleotides, which are efficient inhibitors of the catalytic activity of integrase, provided that they are conjugated to a hydrophobic compound, acridine. To understand the mechanism of the conjugate inhibitory action, we used a steady-state fluorescence anisotropy assay, which allowed us to study the stability of the integrase/DNA complex in various conditions. We found that oligonucleotide-acridine conjugates induced the efficient dissociation of preassembled integrase/DNA complexes. The simultaneous presence of both acridine and an oligonucleotidic moiety is required for the inhibitory activity of conjugates. However, the dissociation effect is not dependent on the oligonucleotide sequence. Finally, our results suggest that the conjugates bind directly to integrase within its complex with DNA at a site different from the viral DNA binding site.

One-way light propagation through a steplike discontinuity of dielectric-slab waveguide is simulated by using the finite-difference beam-propagation method (FD-BPM) and the Green's function method. The validity of the slowly varying envelope approximation in modeling of the total field distribution and the radiation-field distribution is analyzed. © 2004 Wiley Periodicals, Inc. Microwave Opt Technol Lett 41: 108–114, 2004; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/mop.20063

The effect of the second-order dispersion on the spatiotemporal dynamics of ultrashort pulses in nonlinear waveguides with infinite parabolic and stepped profiles of the refractive index is studied. It is shown that the leakage of radiation from the core to the cladding of step-index waveguides prevents the formation of a steady spatiotemporal distribution of the field. The possibility of compressing light pulses in a dielectric waveguide with a positive group-velocity dispersion is discussed.

A nonstationary two-dimensional problem of propagation of a femtosecond pulse in a planar waveguide comprised of linear and nonlinear sections connected in series is solved using the finite-difference method. The accuracy of the finite-difference techniques is analyzed as applied to solution of stationary and nonstationary two-dimensional quasi-linear equations of light propagation in step-index waveguides. The effects of wave instability on the dynamics of the spatiotemporal pulse distribution in a nonlinear waveguide are studied. It is shown that, due to the retarded nonlinear response of the medium and the dependence of the group velocity of the pulse on its intensity, radiation continuously leaks from the fiber core to the cladding as the pulse propagates along the fiber.

Mechanisms that regulate neurite outgrowth are phylogenetically conserved, including the signaling molecules involved. Here, we describe neurotrophic effects on isolated bag cell neurons (BCNs) of substrate-bound growth factors endogenous to the sea slug Aplysia californica. Sheath cells dissociated from the pleural-visceral connectives of the Aplysia CNS and arterial cells dissociated from the anterior aorta enhance neurite outgrowth when compared to controls, i.e., BCNs grown in defined medium alone. In addition, the substrate remaining after sheath cells or arterial cells are killed significantly enhances growth, relative to all other conditions tested. For instance, primary neurites are more numerous and greater in length for BCNs cultured on substrate produced by arterial cells. These results suggest that sheath and arterial cells produce growth-promoting factors, some of which are found in the substrates produced by these cell types. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), we found that Aplysia collagen-like peptides are produced by dissociated arterial cells, and therefore likely contribute to the observed growth effects. Collagen-like peptides and other factors produced by sheath and arterial cells likely influence neurite growth in the Aplysia CNS during development, learning and memory, and regeneration after injury.

Conjugates of amines or short peptides with oligonucleotides containing 5'-terminal carboxyl group were prepared by solid phase chemical synthesis. A correlation between the physicochemical parameters and retention times of the synthesized conjugates was established by ion-pair reversed-phase HPLC.

The synthesis of oligodeoxyribonucleotides bearing mono- and diphosphoryldisulfide internucleotide links was optimized. Oligonucleotide 3"-phosphorothioates were modified using the thiophosphoryl–disulfide exchange with preactivated 5"-deoxy-5"-mercaptooligonucleotides or 5"-phosphorothioate derivatives both with and without a complementary template. The lack of template was shown to differently affect the product ratio (homo- and heterodimers) in the reactions of mono- and diphosphoryldisulfide-containing oligonucleotides. A replacement of one natural phosphodiester bond in 15–16-mer duplexes by a mono- or diphosphoryldisulfide group causes a slight thermal destabilization of the corresponding duplex. The disulfide recombination of the resulting compounds was studied.

An efficient method for synthesis of oligonucleotide 5′-conjugates through amide-bond formation on solid phase is described. Protected oligonucleotides containing a 5′-carboxylic acid function were obtained by use of a novel non-nucleosidic phosphoramidite building block, where the carboxylic acid moiety was protected by a 2-chlorotrityl group. The protecting group is stable to the phosphoramidite coupling conditions used in solid-phase oligonucleotide assembly, but is easily deprotected by mild acidic treatment. The protecting group may be removed also by ammonolysis. 5′-Carboxylate-modified oligonucleotides were efficiently conjugated on solid support under normal peptide-coupling conditions to various amines or to the N-termini of small peptides to yield products of high purity. The method is well-suited in principle for the synthesis of peptide-oligonucleotide conjugates containing an amide linkage between the 5′-end of an oligonucleotide and the N-terminus of a peptide.

Eigenvalue equations for rigorous HE1n and scalar LP0n modes of a step-index fibre are solved numerically above and below the cutoff frequency with account of material losses in the fibre cladding. Polarisation corrections to transverse wavenumbers of the LP02 mode are calculated. Behaviour of dispersion curves in a complex plane of transverse wavenumber in cladding is taken as a basis of the analysis. Transmittance of a lossy fibre junction consisting of the single-mode and bimodal segments is evaluated. Error in the scalar approximation is proved to increase significantly near the cutoff frequency. 2002 Elsevier Science B.V. All rights reserved.

The published data on the synthesis of 2'-O-alkylnucleosides are reviewed. The known methods are systematised and their advantages and disadvantages are discussed. The bibliography includes 174 references.

2'-Deoxyoligonucleotides and 2'-O-methyloligoribonucleotides carrying one or more 2'-aldehyde groups were synthesized and coupled to peptides containing an N-terminal cysteine, aminooxy, or hydrazide group to give peptide-oligonucleotide conjugates incorporating single or multiple peptides in good yield. The facile conjugation method allows specific coupling in aqueous solution of unprotected oligonucleotides containing aldehyde groups to unprotected N-terminally modified peptides and other small molecules. A 12-mer 2'-O-methyloligoribonucleotide complementary to the HIV-1 TAR RNA stem-loop and containing two conjugated copies of an 8-mer model laminin peptide was hardly affected in TAR RNA binding and showed a similar level of inhibition of HIV-1 Tat-dependent in vitro transcription compared to the unconjugated 2'-O-methyloligoribonucleotide. Advantages of this conjugation method include (1) the ability to attach more than one peptide or other small molecule to oligonucleotide at defined nucleoside residue locations; (2) a conjugation route that does not affect significantly oligonucleotide binding to RNA structures; and (3) three alternative, facile, and mild conjugation reaction types that do not require use of a large excess of peptide reagent.